Endogenous retrovirus expression is associated with response to immune checkpoint blockade in clear cell renal cell carcinoma

Abstract

Although a subset of clear cell renal cell carcinoma (ccRCC) patients respond to immune checkpoint blockade (ICB), predictors of response remain uncertain. We investigated whether abnormal expression of endogenous retroviruses (ERVs) in tumors is associated with local immune checkpoint activation (ICA) and response to ICB. Twenty potentially immunogenic ERVs (πERVs) were identified in ccRCC in The Cancer Genome Atlas data set, and tumors were stratified into 3 groups based on their expression levels. πERV-high ccRCC tumors showed increased immune infiltration, checkpoint pathway upregulation, and higher CD8+ T cell fraction in infiltrating leukocytes compared with πERV-low ccRCC tumors. Similar results were observed in ER+/HER2- breast, colon, and head and neck squamous cell cancers. ERV expression correlated with expression of genes associated with histone methylation and chromatin regulation, and πERV-high ccRCC was enriched in BAP1 mutant tumors. ERV3-2 expression correlated with ICA in 11 solid cancers, including the 4 named above. In a small retrospective cohort of 24 metastatic ccRCC patients treated with single-agent PD-1/PD-L1 blockade, ERV3-2 expression in tumors was significantly higher in responders compared with nonresponders. Thus, abnormal expression of πERVs is associated with ICA in several solid cancers, including ccRCC, and ERV3-2 expression is associated with response to ICB in ccRCC.

Keywords: Immunology; Immunotherapy; Oncology.

Conflict of interest statement

Conflict of interest: The authors have declared that no conflict of interest exists.

Figures

Figure 1. Potentially immunogenic ERVs are abundant in 4 solid cancers from TCGA.

(A) Immune checkpoint activation criteria used to identify potentially immunogenic ERVs (πERVs) in each solid cancer type. (B) The number of πERVs in each solid cancer type identified 4 cancer types with an unusually high number of πERVs. (C) Correlation (Spearman) between expression of πERVs (rows) and levels of immunological variables (columns) in the 4 cancer types. (D) ERV3-2 was identified as a πERV in 11 different cancer types. Cancer type acronyms are standard TCGA abbreviations (https://tcga-data.nci.nih.gov/).

Figure 2. Expression of πERVs defines subtypes with differential immune checkpoint activation in ccRCC (KIRC).

(A) Hierarchical clustering of tumors from TCGA (columns) by expression (percentile) of πERVs (rows) stratifies tumors into 3 subtypes (high [H], intermediate [I], and low [L]). (B) Frequency of VHL, PBRM1, SETD2, and BAP1 mutations (dark, truncating mutations; light, other nonsynonymous mutations) in the 3 subtypes. Comparison of (C) overall immune infiltration in tumors (“ImmuneScore”) and fractional composition of tumor-infiltrating leukocytes and (D) mRNA expression of CD8A (cytotoxic T cell marker) and immune checkpoint genes between πERV-high and πERV-low subtypes. Number of samples: (C) ImmuneScore (119 H, 228 L), all other categories (90 H, 134 L), (D) 119 H and 228 L. P values reported in bar plots and box plots are from Fisher’s exact test and Wilcoxon rank-sum test, respectively (all 2 sided). *P < 0.05, **P < 10–3, ***P < 10–6.

Figure 3. RNA expression of ERV3-2 predicts the response to immune checkpoint blockade in ccRCC.

(A) Expression of ERV3-2 is significantly higher in tumors from responders compared with tumors from nonresponders and is an excellent predictor of response to immune checkpoint blockade for both primers. Green arrows mark the optimal cutoffs that were subsequently used to stratify patients into ERV3-2+ or ERV3-2− groups for consistency checks. (B) The ERV3-2+ group has significantly higher objective response rates and longer progression-free survival compared with the ERV3-2− group for both primers. (C) In contrast, πERV-high/intermediate subtypes have shorter overall survival under standard therapy compared with πERV-low subtype in TCGA ccRCC (KIRC) cohort. The number of samples is specified in each panel. P values reported in bar plots, box plots, and Kaplan-Meier plots are from Fisher’s exact test, Wilcoxon rank-sum test, and log-rank tests, respectively (all 2 sided).